SPARC Terminology

If a term does not exist in either ontology (UBERON or FMA), it is added to a tool built by the team at UCSD  - InterLex. InterLex is a lexicon/dictionary of biomedical terms that provides a master resource to search medical/biological terms. Learn more about InterLex from and it's use within SPARC here. This tool integrates existing terminologies, lexicons, and ontologies to allow for mapping between these terms. Additionally, under the SAWG recommendation, this knowledge is contributed back to community ontologies to enhance their coverage of CNS-PNS-Organ interactions.

The SPARC organ-specific term lists can be viewed here,  after clicking on the "relationships" tab. 

A SPARC term request can be submitted here.

Anatomy knowledge deals with the precise relationship between a human-readable anatomical term/label and the definition of that region (e.g. in the heart, community-wide consensus needs to be reached on the concept label/term “mitral valve” and the definition of what it is/what its boundaries are/over which range of organisms does homology of this structure hold). In addition, the identification (and, therefore, definition) of certain structures (e.g. subcellular) is dependent on a particular combination of preparing/staining/imaging/image processing techniques (i.e. a protocol). The navigation of such a wide combinatorial space of concepts, labels, definitions and protocols spawns a heterogeneity of approaches and, in consequence, opinions.

In this context, the SAWG provides community-supported leadership and arbitration on the accepted relationship between anatomical label and definition (and, by extension, the relationship between concepts - i.e. between a label-definition couplet and another).

In addition, part of this arbitration is to recommend and reconcile different topographical atlases that capture labelled regions within a coordinate system for some organ.

Another part of this arbitration is manifest via the term-request pipeline, in which a curator who has not found an appropriate label with which to annotate an image sub-region can submit a new term for global use within SPARC (and beyond). 

1. Documentation for adding terms to the SPARC vocabularies.
   • SPARC has several methods for adding terms to the SPARC vocabularies, depending on the number of terms to be added. An overview of how to add to the SPARC vocabularies provides detailed instructions.
   • For internal or advanced users who are familiar with the process, you can access the InterLex webpage here.
   • Instructions to submit a term request, is located here.
2. SPARC vocabulary-building instructions
   • Slide presentation outlining the strategy and procedures for building the SPARC vocabularies are located here
     • We keep a master list of all terms that have been added to Interlex by SPARC researchers for annotation of data, flatmaps or models. Each of these terms are reviewed by a knowledge curator to determine whether or not the term may already exist (for example, it might be a synonym of an existing term) or whether it should be formally added to the SPARC vocabularies. The SAWG, comprised of SPARC researchers and outside experts, provides advice to the knowledge curators about vocabulary additions.
3. Adoption of InterLex terminology services (for developers)
   • Ontology documentation
4. Up-to-date listing of terms applied to SPARC1 metadata annotation
   • Term code
   • Organ-specific term lists
     
   • All Terms
5. Up-to-date listing of terms applied to flatmap metadata annotation
   • flatmap metadata annotation 
6. Up-to-date listing of terms applied to ApiNATOMY metadata annotation google sheet